Variant report

Variant	rs12739243
Chromosome Location	chr1:210302043-210302044
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10863810	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11119399	0.93[AMR][1000 genomes]
rs11119421	0.86[AMR][1000 genomes]
rs11119422	0.85[AMR][1000 genomes]
rs11119423	0.82[AMR][1000 genomes]
rs12029138	0.88[AMR][1000 genomes]
rs2046850	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2046851	0.92[ASN][1000 genomes]
rs4271216	0.87[AMR][1000 genomes]
rs4537554	0.86[AMR][1000 genomes]
rs4609425	0.88[AMR][1000 genomes]
rs7516843	0.85[AMR][1000 genomes]
rs7527845	0.85[AMR][1000 genomes]
rs7535045	0.88[AMR][1000 genomes]
rs7536761	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7545279	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv873140	chr1:210068117-210335644	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873144	chr1:210252522-210347417	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv818800	chr1:210258653-210304319	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12739243	SLC30A1	cis	cerebellum	SCAN
rs12739243	PFKFB2	cis	cerebellum	SCAN
rs12739243	IL24	cis	cerebellum	SCAN
rs12739243	SYT14	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210298400-210318200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:210299600-210305800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:210302000-210303400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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